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Changed output file to be user-defined 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5149 348d0f76-0448-11de-a6fe-93d51630548a
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fromer 2011-01-31 22:15:26 +00:00
parent 391f248640
commit 742bd44728
1 changed files with 5 additions and 2 deletions
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7
scala/qscript/oneoffs/fromer/phaseSamples.scala
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@ -36,6 +36,9 @@ class PhaseSamples extends QScript {
@Input(doc="Samples to phase together. By default is set to 1 [one job per sample].", shortName="samplesPerJob", required=false) @Input(doc="Samples to phase together. By default is set to 1 [one job per sample].", shortName="samplesPerJob", required=false)
var samplesPerJob = 1 var samplesPerJob = 1
@Input(doc="Phased file to output", shortName="o", required=true)
var outputPhased: File = _
trait CommandLineGATKArgs extends CommandLineGATK { trait CommandLineGATKArgs extends CommandLineGATK {
this.intervalsString = List(qscript.intervals) this.intervalsString = List(qscript.intervals)
this.jarFile = qscript.gatkJarFile this.jarFile = qscript.gatkJarFile
@ -46,7 +49,7 @@ class PhaseSamples extends QScript {
// A target has a list of samples and bam files to use for phasing // A target has a list of samples and bam files to use for phasing
class Target(val name: String, val samples: List[String], val bams: List[File]) { class Target(val name: String, val samples: List[String], val bams: List[File]) {
def phasedVCFFile = new File(name + ".phased.vcf") def phasedVCFFile = new File(name + "." + outputPhased)
override def toString(): String = String.format("[Target %s with samples %s against bams %s]", name, samples, bams) override def toString(): String = String.format("[Target %s with samples %s against bams %s]", name, samples, bams)
} }
@ -119,7 +122,7 @@ class CombineVariants(vcfsToCombine: List[File]) extends org.broadinstitute.stin
this.variantMergeOptions = Some(org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils.VariantMergeType.UNION) this.variantMergeOptions = Some(org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils.VariantMergeType.UNION)
this.out = new File("phased.vcf") this.out = new File(outputPhased)
} }
} }